1. iPortal Ease of use and scale-up of Workflows for Proteomics Analysis
Lorenz Blum

2. Synopsis
Web portal for simple submission of complex proteomics workflows
Used by scientists at ETHZ and Lund University
Developed as part of the SCI-BUS project

3. iPortal for developers
Assembly of workflows
Split, merge, join, embedding, conditional execution
Workflow submission for many backends and supports "high-throughput"

4. iPortal for Users

5. New Functions Automated workflow testing
Simplified reference FASTA upload

6. New Workflows
Spectral reference library creation
OpenSWATH analysis

7. SWATH MS/MS

8. [ [ SWATH MS/MS * MS/MS mode SWATH mode 25Da Collision Cell Isolation
m/z *
200
400
600
800
1000
1200
Isolation
Fragmentation
Analysis
Tandem mass spectrum
SWATH mode
Collision Cell
Analyzer 1
Analyzer 2 [
m/z [
25Da

9. SWATH MS/MS Data-Independent Acquisition
Complete measurement of every sample
Unbiased recording
Quantitative MS/MS data for all peptides

10. SWATH MS/MS

11. OpenSWATH Workflow 1 sample: 20 GB spectral data
Normalize
Analyze
Group features
1 sample:
20 GB spectral data
few GB temporary files
5 h runtime

12. Scalability Yansheng Liu 246 samples 5 TB of spectra (mzXML)
1.5 TB temporary files
2000 job submissions
40'000 CPU hours
41 h runtime (23 h in alignment)
analysis in progress…